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- PDB-2h7r: L244A mutant of Cytochrome P450cam complexed with imidazole -

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Basic information

Entry
Database: PDB / ID: 2h7r
TitleL244A mutant of Cytochrome P450cam complexed with imidazole
ComponentsCytochrome P450-cam
KeywordsOXIDOREDUCTASE / Azole drugs / imidazole binding / cytochrome P450 inhibition / protein maleability / active site conformation
Function / homology
Function and homology information


camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1-METHYLIMIDAZOLE / PROTOPORPHYRIN IX CONTAINING FE / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVerras, A. / Alian, A. / Montellano, P.R.
CitationJournal: Protein Eng.Des.Sel. / Year: 2006
Title: Cytochrome P450 active site plasticity: attenuation of imidazole binding in cytochrome P450cam by an L244A mutation.
Authors: Verras, A. / Alian, A. / Montellano, P.R.
History
DepositionJun 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450-cam
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2143
Polymers46,5151
Non-polymers7002
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.599, 58.784, 57.441
Angle α, β, γ (deg.)90.00, 105.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450-cam / Camphor 5-monooxygenase / P450cam


Mass: 46514.738 Da / Num. of mol.: 1 / Mutation: L244A, C334A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Production host: Escherichia coli (E. coli) / References: UniProt: P00183, camphor 5-monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-1MZ / 1-METHYLIMIDAZOLE


Mass: 83.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 50mM Potassium phosphate, pH 7.4, 250mM KCL, 50 mM dithiothreitol, 36-52% ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 18642 / Num. obs: 16106 / % possible obs: 86.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rsym value: 0.072 / Net I/σ(I): 12.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 18642 / Rsym value: 0.36 / % possible all: 94.3

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Processing

Software
NameClassification
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1PHC

1phc


Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2835 1603 RAMDOM
Rwork0.2103 --
all0.2103 18642 -
obs0.2103 16106 -
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 49 114 3359
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2.1→2.18 Å
RfactorNum. reflection
Rfree0.21 1603
Rwork0.2835 -
obs-16106

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